Contacts of the helix formed by residues 196 - 201 (chain E) in PDB entry 5J0Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 196 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LYS* 3.5 27.9 - - - +
249A THR 3.4 24.4 + - - -
193E GLN 4.2 5.7 + - - -
195E PHE* 1.3 83.0 - - - +
197E TYR* 1.3 85.5 + - - +
199E PRO* 3.2 10.1 - - - +
200E ASN* 3.1 33.3 - - - +
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Residues in contact with TYR 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LYS* 3.3 35.5 + - + +
119E TYR* 3.1 39.7 + + - -
120E PRO* 3.6 37.0 - - + -
192E ARG* 3.9 18.7 + - - -
193E GLN 4.2 6.3 - - - -
194E TYR* 3.0 20.1 + - - +
195E PHE 2.9 0.6 + - - -
196E SER* 1.3 97.3 + - - +
198E ILE* 1.3 63.2 + - + +
200E ASN* 4.6 1.6 - - - -
201E ILE* 3.1 34.5 + - + +
202E ILE* 3.0 32.1 + - + +
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Residues in contact with ILE 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E PHE* 4.5 8.7 - - + -
194E TYR* 3.7 34.5 - - + +
195E PHE* 3.0 16.4 + - + +
197E TYR* 1.3 79.7 - - - +
199E PRO* 1.4 69.7 - - + +
200E ASN 3.3 0.2 - - - -
202E ILE* 3.2 22.7 + - + -
203E LEU* 2.9 53.3 + - + +
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Residues in contact with PRO 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASN* 5.3 1.9 + - - -
252A MET* 4.0 32.5 - - + -
259A ILE* 6.2 0.2 - - - +
260A PHE* 3.5 49.5 - - + +
195E PHE* 3.2 21.1 - - + +
196E SER* 3.2 7.0 - - - +
198E ILE* 1.4 97.3 - - + +
200E ASN* 1.3 69.0 + - - +
203E LEU* 4.4 0.2 - - + -
204E PRO* 3.6 12.2 - - - +
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Residues in contact with ASN 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASN* 4.4 9.5 + - - +
243A GLU* 3.4 42.1 + - + +
248A LYS* 5.8 4.6 - - - +
252A MET* 5.6 1.6 - - - +
256A GLY* 5.5 5.7 - - - +
196E SER* 3.1 29.7 + - - +
197E TYR* 4.6 1.8 - - - -
198E ILE 3.3 0.4 - - - -
199E PRO* 1.3 92.3 - - - +
201E ILE* 1.3 68.5 + - + +
204E PRO* 3.9 5.0 - - - +
238E PHE* 3.9 16.1 - - - -
241E LEU* 5.6 0.2 - - - +
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Residues in contact with ILE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU* 5.0 7.4 - - - +
248A LYS* 5.6 2.0 - - - -
197E TYR* 3.1 40.2 + - + +
200E ASN* 1.3 86.5 - - + +
202E ILE* 1.3 69.3 + - + +
203E LEU 3.7 0.9 - - - -
204E PRO* 3.8 2.5 - - - +
205E MET* 2.9 48.6 + - + +
238E PHE* 4.3 8.2 - - + +
241E LEU* 4.8 17.9 - - + -
242E VAL* 3.7 34.1 - - + -
245E ASN* 4.4 8.3 - - - +
255E THR* 5.4 7.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il